CHARMM molecular analysis

K Kuezera, JK Wiorkiewicz, M Karplus. MOLVIB Program for the Analysis of Molecular Vibrations, CHARMM, Harvard University, 1993. 

For the construction of molecular structures, a 2D formula editor is provided in combination with 3D conversion. Standard potential energy minimization is performed using the modified parameter set of the CHARMm force field [68] the conformational models are built using Monte Carlo conformational analysis together with poling as described in the next section. 

G. Wu, D. H. Robertson, C. L. Brooks, Detailed analysis of grid-based molecular docking A case study of CDOCKER-A CHARMm-based MD docking algorithm, J. Comput. Chem. 2003, 24, 1549-1562. 

The SHAPES force field" has been implemented in CHARMM and used to examine the structures of several square planar rhodium complexes. This force field is based on angular overlap considerations and treats angular distortions for a variety of geometries. Spherical internal coordinates and Fourier potential functions form the basis for the description of these molecular shapes. The parameters for this force field were derived from normal coordinate analysis, ab initio calculations, and structure-based optimizations. The average rms deviation for bond lengths was 0.026 A, and the average rms deviation for bond angles was 3.2°. 

Tel. 358-0-4572378, fax 358-0-4572302, e-mail leif.laaksonen csc.fi Analysis of molecular simulation trajectories for CHARMM, Discover, YASP, MUMOD, GROMOS, and AMBER. Interface to ICONS for extended Hiickel calculations and to VSS for electrostatic potentials. 2D graphics of surfaces and electron density and orbitals. Silicon Graphics. 

Wu, G.S., Robertson, D.H., Brooks, C.L, and Vieth, M. (2003) Detailed analysis of grid-based molecular docking a case study of CDOCKER - a CHARMm-based MD docking algorithm. Journal of Computational Chemistry, 24, 1549—1562. 

Minimization and vibrational analysis are useful for the determination of force field parameters, system preparation, and the study of many problems of biological interest. A new optimizer based on a truncated Newton method (TNPACK) that is effective for large molecules has been added to CHARMM. All minimizers, excluding TNPACK, support the use of holonomic constraints on selected bonds and angles (SHAKE). Vibrational analysis has been extended via addition of the MOLVIB module (K. Kuczera and J. Wiorkiewicz-Kuczera, unpublished), which allows for the determination of potential energy distributions and the analysis of lattice modes in combination with the CRYSTAL facility. Minimizations may also be performed in the presence of a variety of structural constraints. This allows for atomic positions, internal coordinates, interatomic distances, etc. to be fixed or constrained to specified values. Such constraint methods may be used in molecular dynamics simulations. 

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